Working with HPO Annotations

Phenol ingests the phenotype.hpoa file to get information about diseases including HPO Frequency information. See the documentation for more information about this file.

Parsing Annotation Files

You can parse the phenotype-to-disease annotation files as follows.

import org.monarchinitiative.phenol.ontology.data.TermId;
import org.monarchinitiative.phenol.formats.hpo.HpoDisease;
import org.monarchinitiative.phenol.io.obo.hpo.HpoDiseaseAnnotationParser;
HpoDiseaseAnnotationParser annotationParser =
    new HpoDiseaseAnnotationParser(phenotypeAnnotationPath,ontology);
try {
  Map<TermId, HpoDisease> diseaseMap = annotationParser.parse();
  if (!annotationParser.validParse()) {
        int n = annotationParser.getErrors().size();
          logger.warn("Parse problems encountered with the annotation file at {}. Got {} errors",
                this.phenotypeAnnotationPath,n);
  }
  return diseaseMap; // or do something else with the data
} catch (PhenolException e) {
      e.printStackTrace(); // or do something else
}

Parsing Annotation Files for Specific Sources

To limit the import to data representing diseases in the DECIPHER database, use the following code (the rest is identical). Currently, DECIPHER, OMIM, and ORPHA are available.

List<String> desiredDatabasePrefixes=ImmutableList.of("DECIPHER");
HpoDiseaseAnnotationParser annotationParser =
    new HpoDiseaseAnnotationParser(phenotypeAnnotationPath,ontology,desiredDatabasePrefixes);